Proper control of gene expression is essential for life. While substantial advances have been made in the discovery of DNA sequences and transcription factors that act combinatorially to regulate transcription, much less is known about later steps in the gene expression program. Nevertheless, it is now clear that substantial regulation of gene expression occurs post-transcriptionally, in pre-mRNA splicing, RNA transport, RNA localization, translation, and RNA decay, and in the coordination of RNAs by RNA binding proteins (RBPs). Further, recent findings of widespread transcription noncoding RNAs (ncRNA) and of the involvement of these RNAs in critical biological processes such as development and gene regulation suggest the existence of important classes of regulatory RNAs that we are just beginning to explore. The long term goal of this project is to enable structural characterization of RNAs on a genome-wide scale. First, we will apply a recently developed method to map secondary structures of most human RNAs. Second, we will examine how RNA secondary structures contribute to the functions of human long intergenic noncoding RNAs. Third, we will develop computational and experimental methods to further improve the precision and scope of genome-scale measurements of RNA structures. This integrated pipeline of new experimental and computational tools will enable investigators to identify and decode regulatory RNA elements in the genome with unprecedented speed and accuracy.